gt.result-class {globaltest} | R Documentation |
Class "gt.result" for results of the function globaltest
Description
The class gt.result is the output of a call to
globaltest
and the input of various plotting
functions to visualize the test result.
Slots
res
:- Object of class "matrix". Test results summary.
eX
:- Object of class "matrix". The transformed data matrix.
genesets
:- A list of vectors indicating the tested genes.
IminH
:- Object of class "matrix". Needed when drawing the various
diagnostic plots.
fit
:- Object of class "list". This list contains one element which is of class "lm",
"glm", "coxph" or "coxph.null". Thhis latter object contains the fitted model of the null hypothesis.
PermQs
:- Object of class "matrix". Stores the permuted test
statistics generated by a call to
permutations
.
SamplingZs
:- Object of class "list". Stores the standardized test statistics of random gene sets generated by
a call to
sampling
.
Methods
- show
- (gt.result): Summarizes the test result.
- "["
- (gt.result): Extracts results of one or more
pathways if multiple pathways were tested.
- length
- (gt.result): The number of pathways tested.
- size
- (gt.result): Extracts a vector with the number of genes tested for each pathway.
- p.value
- (gt.result): Extracts the p-values.
- z.score
- (gt.result): Extracts z-score (Q - EQ) / sd(Q).
- sort
- (gt.result): Sorts the pathways to increasing p-values.
- result
- (gt.result): Extracts the results matrix.
- names
- (gt.result): Extracts the pathway names.
- names<-
- (gt.result): Changes the pathway names.
- combine
- (gt.result): Combines two {gt.result} objects to one,
provided the data and model match.
- fit
- (gt.result): Extracts the fitted (adjust)model.
- hist
- (gt.result): Produces a histogram to visualize the
permutations generated by
permutations
.
- geneplot
- (gt.result): The
geneplot
produces
a plot to show the influence of individual
genes on the test result produced by globaltest
.
- sampleplot
- (gt.result): The
sampleplot
produces a plot to show the influence of individual
samples on the test result produced by globaltest
.
- permutations
- (gt.result): The function
permutations
recalculates the p-values using permutations of the outcome Y.
- sampling
- (gt.result): The function
sampling
compares the p-values with p-values of randomly
generated pathways.
- checkerboard
- (gt.result): Produces a plot to visualize the test result
produced by
globaltest
by showing the association
between pairs of samples.
- regressionplot
- (gt.result): Produces a plot which can be used to visualize
the effect of specific samples on the test result produced by
globaltest
.
Author(s)
Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting
See Also
globaltest
, sampleplot
,
geneplot
, permutations
.
[Package
globaltest version 4.6.0
Index]